Starting phenix.real_space_refine on Fri Mar 6 05:16:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v3g_21036/03_2026/6v3g_21036.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v3g_21036/03_2026/6v3g_21036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v3g_21036/03_2026/6v3g_21036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v3g_21036/03_2026/6v3g_21036.map" model { file = "/net/cci-nas-00/data/ceres_data/6v3g_21036/03_2026/6v3g_21036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v3g_21036/03_2026/6v3g_21036.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 18456 2.51 5 N 4680 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28520 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 7130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7130 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 866} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: A, C, D Time building chain proxies: 7.36, per 1000 atoms: 0.26 Number of scatterers: 28520 At special positions: 0 Unit cell: (144.3, 144.3, 135.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 5192 8.00 N 4680 7.00 C 18456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6800 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 49.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 22 through 34 removed outlier: 3.934A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 134 removed outlier: 3.823A pdb=" N ARG B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.639A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.529A pdb=" N LEU B 179 " --> pdb=" O TRP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 removed outlier: 4.631A pdb=" N TYR B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.765A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 211 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.533A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 259 removed outlier: 3.529A pdb=" N SER B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.990A pdb=" N MET B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.797A pdb=" N GLU B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 removed outlier: 3.709A pdb=" N ASN B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.581A pdb=" N HIS B 468 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.551A pdb=" N LYS B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 765 through 770 removed outlier: 5.434A pdb=" N GLU B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 792 removed outlier: 3.781A pdb=" N LEU B 789 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 816 Processing helix chain 'B' and resid 817 through 830 Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.587A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.717A pdb=" N ASN B 887 " --> pdb=" O ASN B 884 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 884 through 888' Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 919 through 930 removed outlier: 3.751A pdb=" N LEU B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 942 Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR B1006 " --> pdb=" O LYS B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1021 removed outlier: 3.671A pdb=" N ALA B1020 " --> pdb=" O LEU B1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS B1021 " --> pdb=" O ARG B1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1017 through 1021' Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.933A pdb=" N SER A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 134 removed outlier: 3.822A pdb=" N ARG A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.639A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.528A pdb=" N LEU A 179 " --> pdb=" O TRP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 removed outlier: 4.632A pdb=" N TYR A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.765A pdb=" N ARG A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 211 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.532A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 259 removed outlier: 3.529A pdb=" N SER A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.990A pdb=" N MET A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 removed outlier: 3.796A pdb=" N GLU A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.708A pdb=" N ASN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.580A pdb=" N HIS A 468 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.625A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.550A pdb=" N LYS A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 759 through 764 Processing helix chain 'A' and resid 765 through 770 removed outlier: 5.433A pdb=" N GLU A 768 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.780A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 816 Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.586A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.717A pdb=" N ASN A 887 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 888' Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 919 through 930 removed outlier: 3.752A pdb=" N LEU A 923 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1021 removed outlier: 3.671A pdb=" N ALA A1020 " --> pdb=" O LEU A1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS A1021 " --> pdb=" O ARG A1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1017 through 1021' Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.934A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 134 removed outlier: 3.823A pdb=" N ARG C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.638A pdb=" N ALA C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 175 through 179 removed outlier: 3.529A pdb=" N LEU C 179 " --> pdb=" O TRP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 removed outlier: 4.632A pdb=" N TYR C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.765A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 211 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.533A pdb=" N ILE C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 removed outlier: 3.528A pdb=" N SER C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.990A pdb=" N MET C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 removed outlier: 3.797A pdb=" N GLU C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 removed outlier: 3.709A pdb=" N ASN C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.581A pdb=" N HIS C 468 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 532 " --> pdb=" O TYR C 528 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 610 No H-bonds generated for 'chain 'C' and resid 608 through 610' Processing helix chain 'C' and resid 621 through 626 removed outlier: 3.551A pdb=" N LYS C 626 " --> pdb=" O PRO C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 765 through 770 removed outlier: 5.434A pdb=" N GLU C 768 " --> pdb=" O ARG C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 removed outlier: 3.781A pdb=" N LEU C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 816 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.587A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 removed outlier: 3.717A pdb=" N ASN C 887 " --> pdb=" O ASN C 884 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 888 " --> pdb=" O ASP C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 884 through 888' Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 919 through 930 removed outlier: 3.752A pdb=" N LEU C 923 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 942 Processing helix chain 'C' and resid 946 through 954 Processing helix chain 'C' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1021 removed outlier: 3.672A pdb=" N ALA C1020 " --> pdb=" O LEU C1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS C1021 " --> pdb=" O ARG C1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1017 through 1021' Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.934A pdb=" N SER D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 134 removed outlier: 3.823A pdb=" N ARG D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL D 116 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.639A pdb=" N ALA D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.530A pdb=" N LEU D 179 " --> pdb=" O TRP D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 removed outlier: 4.631A pdb=" N TYR D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.766A pdb=" N ARG D 210 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 211 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.532A pdb=" N ILE D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 259 removed outlier: 3.528A pdb=" N SER D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.989A pdb=" N MET D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 326 removed outlier: 3.797A pdb=" N GLU D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 removed outlier: 3.709A pdb=" N ASN D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.581A pdb=" N HIS D 468 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU D 530 " --> pdb=" O LYS D 526 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D 532 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 610 No H-bonds generated for 'chain 'D' and resid 608 through 610' Processing helix chain 'D' and resid 621 through 626 removed outlier: 3.550A pdb=" N LYS D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 759 through 764 Processing helix chain 'D' and resid 765 through 770 removed outlier: 5.435A pdb=" N GLU D 768 " --> pdb=" O ARG D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 removed outlier: 3.780A pdb=" N LEU D 789 " --> pdb=" O SER D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 816 Processing helix chain 'D' and resid 817 through 830 Processing helix chain 'D' and resid 872 through 876 removed outlier: 3.587A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.718A pdb=" N ASN D 887 " --> pdb=" O ASN D 884 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 888 " --> pdb=" O ASP D 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 884 through 888' Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 919 through 930 removed outlier: 3.752A pdb=" N LEU D 923 " --> pdb=" O VAL D 919 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 942 Processing helix chain 'D' and resid 946 through 954 Processing helix chain 'D' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR D1006 " --> pdb=" O LYS D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1021 removed outlier: 3.671A pdb=" N ALA D1020 " --> pdb=" O LEU D1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS D1021 " --> pdb=" O ARG D1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1017 through 1021' Processing sheet with id=AA1, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'B' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU B 594 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR B 570 " --> pdb=" O ARG B 578 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 976 through 980 removed outlier: 6.497A pdb=" N PHE B1050 " --> pdb=" O PHE B1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU A 594 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR A 570 " --> pdb=" O ARG A 578 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 976 through 980 removed outlier: 6.498A pdb=" N PHE A1050 " --> pdb=" O PHE A1012 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB3, first strand: chain 'C' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU C 594 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR C 570 " --> pdb=" O ARG C 578 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 976 through 980 removed outlier: 6.497A pdb=" N PHE C1050 " --> pdb=" O PHE C1012 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AB8, first strand: chain 'D' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU D 594 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR D 570 " --> pdb=" O ARG D 578 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 976 through 980 removed outlier: 6.497A pdb=" N PHE D1050 " --> pdb=" O PHE D1012 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3012 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6819 1.33 - 1.45: 6241 1.45 - 1.57: 15828 1.57 - 1.69: 0 1.69 - 1.81: 284 Bond restraints: 29172 Sorted by residual: bond pdb=" N ASN A 582 " pdb=" CA ASN A 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.03e+01 bond pdb=" N ASN B 582 " pdb=" CA ASN B 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.03e+01 bond pdb=" N ASN D 582 " pdb=" CA ASN D 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.03e+01 bond pdb=" N ASN C 582 " pdb=" CA ASN C 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.02e+01 bond pdb=" N ILE C 568 " pdb=" CA ILE C 568 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.11e-02 8.12e+03 9.99e+00 ... (remaining 29167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 35484 1.66 - 3.33: 3525 3.33 - 4.99: 458 4.99 - 6.66: 81 6.66 - 8.32: 32 Bond angle restraints: 39580 Sorted by residual: angle pdb=" N GLN D 807 " pdb=" CA GLN D 807 " pdb=" C GLN D 807 " ideal model delta sigma weight residual 112.89 106.80 6.09 1.24e+00 6.50e-01 2.41e+01 angle pdb=" N GLN A 807 " pdb=" CA GLN A 807 " pdb=" C GLN A 807 " ideal model delta sigma weight residual 112.89 106.81 6.08 1.24e+00 6.50e-01 2.41e+01 angle pdb=" N GLN B 807 " pdb=" CA GLN B 807 " pdb=" C GLN B 807 " ideal model delta sigma weight residual 112.89 106.82 6.07 1.24e+00 6.50e-01 2.40e+01 angle pdb=" N GLN C 807 " pdb=" CA GLN C 807 " pdb=" C GLN C 807 " ideal model delta sigma weight residual 112.89 106.82 6.07 1.24e+00 6.50e-01 2.39e+01 angle pdb=" O ILE C 625 " pdb=" C ILE C 625 " pdb=" N LYS C 626 " ideal model delta sigma weight residual 121.87 125.76 -3.89 9.70e-01 1.06e+00 1.61e+01 ... (remaining 39575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 16283 15.93 - 31.86: 757 31.86 - 47.79: 164 47.79 - 63.72: 32 63.72 - 79.65: 16 Dihedral angle restraints: 17252 sinusoidal: 6760 harmonic: 10492 Sorted by residual: dihedral pdb=" CA ARG C 742 " pdb=" C ARG C 742 " pdb=" N ALA C 743 " pdb=" CA ALA C 743 " ideal model delta harmonic sigma weight residual 180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG B 742 " pdb=" C ARG B 742 " pdb=" N ALA B 743 " pdb=" CA ALA B 743 " ideal model delta harmonic sigma weight residual 180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG A 742 " pdb=" C ARG A 742 " pdb=" N ALA A 743 " pdb=" CA ALA A 743 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 17249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2905 0.054 - 0.108: 1053 0.108 - 0.161: 354 0.161 - 0.215: 168 0.215 - 0.269: 44 Chirality restraints: 4524 Sorted by residual: chirality pdb=" CA ILE C 484 " pdb=" N ILE C 484 " pdb=" C ILE C 484 " pdb=" CB ILE C 484 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ILE A 484 " pdb=" N ILE A 484 " pdb=" C ILE A 484 " pdb=" CB ILE A 484 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE B 484 " pdb=" N ILE B 484 " pdb=" C ILE B 484 " pdb=" CB ILE B 484 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4521 not shown) Planarity restraints: 4984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 246 " -0.020 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP A 246 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 246 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 246 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 246 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 246 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 246 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 246 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 246 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 246 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 246 " 0.020 2.00e-02 2.50e+03 1.64e-02 6.75e+00 pdb=" CG TRP C 246 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 246 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 246 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 246 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 246 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 246 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 246 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 246 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 246 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 246 " -0.020 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP D 246 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 246 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 246 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 246 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 246 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 246 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 246 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 246 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 246 " -0.002 2.00e-02 2.50e+03 ... (remaining 4981 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3354 2.75 - 3.29: 28552 3.29 - 3.82: 46798 3.82 - 4.36: 56132 4.36 - 4.90: 92504 Nonbonded interactions: 227340 Sorted by model distance: nonbonded pdb=" N GLU C 819 " pdb=" OE1 GLU C 819 " model vdw 2.211 3.120 nonbonded pdb=" N GLU B 819 " pdb=" OE1 GLU B 819 " model vdw 2.212 3.120 nonbonded pdb=" N GLU D 819 " pdb=" OE1 GLU D 819 " model vdw 2.212 3.120 nonbonded pdb=" N GLU A 819 " pdb=" OE1 GLU A 819 " model vdw 2.212 3.120 nonbonded pdb=" N ASP B 621 " pdb=" OD1 ASP B 621 " model vdw 2.217 3.120 ... (remaining 227335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.360 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 29172 Z= 0.480 Angle : 1.052 8.322 39580 Z= 0.694 Chirality : 0.071 0.269 4524 Planarity : 0.006 0.052 4984 Dihedral : 10.567 79.651 10452 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.66 % Allowed : 4.95 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.13), residues: 3548 helix: -2.14 (0.11), residues: 1456 sheet: -2.15 (0.22), residues: 416 loop : -1.28 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1031 TYR 0.025 0.002 TYR D1015 PHE 0.030 0.003 PHE A1012 TRP 0.044 0.002 TRP A 246 HIS 0.013 0.002 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00797 (29172) covalent geometry : angle 1.05218 (39580) hydrogen bonds : bond 0.20127 ( 1072) hydrogen bonds : angle 8.08360 ( 3012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 533 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6226 (mpp) cc_final: 0.5947 (mpp) REVERT: B 491 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8625 (tp) REVERT: B 506 MET cc_start: 0.6557 (ttm) cc_final: 0.6079 (ttp) REVERT: B 627 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7881 (mtmm) REVERT: B 715 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8009 (pp) REVERT: B 795 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8891 (p0) REVERT: B 998 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.7988 (p0) REVERT: A 21 MET cc_start: 0.6220 (mpp) cc_final: 0.5950 (mpp) REVERT: A 491 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 506 MET cc_start: 0.6560 (ttm) cc_final: 0.6088 (ttp) REVERT: A 627 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7878 (mtmm) REVERT: A 715 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8012 (pp) REVERT: A 795 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8885 (p0) REVERT: A 998 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7981 (p0) REVERT: C 21 MET cc_start: 0.6223 (mpp) cc_final: 0.5951 (mpp) REVERT: C 491 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8636 (tp) REVERT: C 506 MET cc_start: 0.6554 (ttm) cc_final: 0.6067 (ttp) REVERT: C 627 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7787 (mtmm) REVERT: C 715 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8004 (pp) REVERT: C 795 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8874 (p0) REVERT: C 998 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8135 (p0) REVERT: D 21 MET cc_start: 0.6227 (mpp) cc_final: 0.5955 (mpp) REVERT: D 491 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8648 (tp) REVERT: D 506 MET cc_start: 0.6550 (ttm) cc_final: 0.6070 (ttp) REVERT: D 627 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7804 (mtmm) REVERT: D 715 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8056 (pp) REVERT: D 795 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8899 (p0) REVERT: D 998 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.7950 (p0) outliers start: 84 outliers final: 14 residues processed: 613 average time/residue: 0.1656 time to fit residues: 162.7613 Evaluate side-chains 292 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 800 CYS Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 632 ARG Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 795 ASN Chi-restraints excluded: chain C residue 800 CYS Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 632 ARG Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 795 ASN Chi-restraints excluded: chain D residue 800 CYS Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN B 258 ASN B 379 HIS B 394 HIS B 501 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN A 136 ASN A 258 ASN A 379 HIS A 394 HIS A 501 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 258 ASN C 379 HIS C 394 HIS C 501 GLN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 ASN C 893 GLN D 136 ASN D 258 ASN D 379 HIS D 394 HIS D 501 GLN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.061052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.046714 restraints weight = 137457.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.048112 restraints weight = 77523.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049093 restraints weight = 52100.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.049765 restraints weight = 40091.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.050269 restraints weight = 33444.758| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29172 Z= 0.158 Angle : 0.682 8.351 39580 Z= 0.347 Chirality : 0.043 0.144 4524 Planarity : 0.005 0.048 4984 Dihedral : 6.457 59.917 3908 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.16 % Allowed : 10.98 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3548 helix: -1.00 (0.12), residues: 1488 sheet: -1.88 (0.24), residues: 420 loop : -0.86 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 735 TYR 0.017 0.001 TYR B 570 PHE 0.027 0.002 PHE D 303 TRP 0.024 0.001 TRP A 246 HIS 0.004 0.001 HIS D 616 Details of bonding type rmsd covalent geometry : bond 0.00350 (29172) covalent geometry : angle 0.68172 (39580) hydrogen bonds : bond 0.04623 ( 1072) hydrogen bonds : angle 5.83191 ( 3012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 329 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7341 (mpp) cc_final: 0.6748 (mpp) REVERT: B 213 ARG cc_start: 0.8934 (mtt180) cc_final: 0.8075 (mmt-90) REVERT: B 252 PHE cc_start: 0.9564 (t80) cc_final: 0.8999 (t80) REVERT: B 303 PHE cc_start: 0.9393 (t80) cc_final: 0.8617 (t80) REVERT: B 318 TYR cc_start: 0.8200 (t80) cc_final: 0.7790 (t80) REVERT: B 442 MET cc_start: 0.9761 (mmm) cc_final: 0.9507 (tpp) REVERT: B 460 MET cc_start: 0.8145 (mmm) cc_final: 0.7206 (mmm) REVERT: B 513 MET cc_start: 0.8971 (mmm) cc_final: 0.8760 (mmm) REVERT: B 565 MET cc_start: 0.8692 (ttp) cc_final: 0.8446 (ptt) REVERT: B 580 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9358 (tt) REVERT: B 726 ASP cc_start: 0.9038 (t70) cc_final: 0.8759 (p0) REVERT: B 779 LEU cc_start: 0.9226 (tp) cc_final: 0.8985 (mm) REVERT: B 998 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8831 (p0) REVERT: A 21 MET cc_start: 0.7331 (mpp) cc_final: 0.6735 (mpp) REVERT: A 213 ARG cc_start: 0.8916 (mtt180) cc_final: 0.8074 (mmt-90) REVERT: A 252 PHE cc_start: 0.9561 (t80) cc_final: 0.9004 (t80) REVERT: A 303 PHE cc_start: 0.9393 (t80) cc_final: 0.8603 (t80) REVERT: A 318 TYR cc_start: 0.8194 (t80) cc_final: 0.7786 (t80) REVERT: A 442 MET cc_start: 0.9769 (mmm) cc_final: 0.9502 (tpp) REVERT: A 460 MET cc_start: 0.8148 (mmm) cc_final: 0.7279 (mmm) REVERT: A 513 MET cc_start: 0.8966 (mmm) cc_final: 0.8762 (mmm) REVERT: A 565 MET cc_start: 0.8687 (ttp) cc_final: 0.8441 (ptt) REVERT: A 580 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9364 (tt) REVERT: A 726 ASP cc_start: 0.9051 (t70) cc_final: 0.8761 (p0) REVERT: A 998 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8882 (p0) REVERT: C 21 MET cc_start: 0.7369 (mpp) cc_final: 0.6770 (mpp) REVERT: C 213 ARG cc_start: 0.8927 (mtt180) cc_final: 0.8056 (mmt-90) REVERT: C 252 PHE cc_start: 0.9581 (t80) cc_final: 0.9061 (t80) REVERT: C 303 PHE cc_start: 0.9387 (t80) cc_final: 0.8656 (t80) REVERT: C 442 MET cc_start: 0.9748 (mmm) cc_final: 0.9498 (tpp) REVERT: C 460 MET cc_start: 0.8118 (mmm) cc_final: 0.7192 (mmm) REVERT: C 513 MET cc_start: 0.9011 (mmm) cc_final: 0.8806 (mmm) REVERT: C 565 MET cc_start: 0.8707 (ttp) cc_final: 0.8478 (ptt) REVERT: C 580 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9352 (tt) REVERT: C 726 ASP cc_start: 0.9069 (t70) cc_final: 0.8808 (p0) REVERT: C 879 ILE cc_start: 0.9534 (mt) cc_final: 0.9227 (tp) REVERT: C 998 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8806 (p0) REVERT: D 21 MET cc_start: 0.7364 (mpp) cc_final: 0.6761 (mpp) REVERT: D 213 ARG cc_start: 0.8934 (mtt180) cc_final: 0.8061 (mmt-90) REVERT: D 252 PHE cc_start: 0.9581 (t80) cc_final: 0.9145 (t80) REVERT: D 303 PHE cc_start: 0.9421 (t80) cc_final: 0.8904 (t80) REVERT: D 442 MET cc_start: 0.9739 (mmm) cc_final: 0.9409 (tpp) REVERT: D 460 MET cc_start: 0.8106 (mmm) cc_final: 0.7179 (mmm) REVERT: D 565 MET cc_start: 0.8709 (ttp) cc_final: 0.8472 (ptt) REVERT: D 580 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9358 (tt) REVERT: D 726 ASP cc_start: 0.9036 (t70) cc_final: 0.8760 (p0) REVERT: D 779 LEU cc_start: 0.9246 (tp) cc_final: 0.9024 (mm) REVERT: D 998 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8807 (p0) outliers start: 68 outliers final: 18 residues processed: 380 average time/residue: 0.1517 time to fit residues: 97.7846 Evaluate side-chains 301 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 46 optimal weight: 0.0060 chunk 274 optimal weight: 10.0000 chunk 210 optimal weight: 0.0470 chunk 143 optimal weight: 0.0170 chunk 197 optimal weight: 6.9990 chunk 342 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 884 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 884 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047675 restraints weight = 137097.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.049034 restraints weight = 77294.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050149 restraints weight = 51156.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.050847 restraints weight = 38690.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051303 restraints weight = 31471.773| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29172 Z= 0.112 Angle : 0.613 8.440 39580 Z= 0.306 Chirality : 0.042 0.159 4524 Planarity : 0.004 0.046 4984 Dihedral : 5.289 50.629 3848 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.74 % Allowed : 11.77 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3548 helix: -0.53 (0.13), residues: 1476 sheet: -1.77 (0.25), residues: 420 loop : -0.73 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 632 TYR 0.012 0.001 TYR A 279 PHE 0.023 0.001 PHE C 164 TRP 0.016 0.001 TRP A 246 HIS 0.003 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00246 (29172) covalent geometry : angle 0.61300 (39580) hydrogen bonds : bond 0.03712 ( 1072) hydrogen bonds : angle 5.43834 ( 3012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 327 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7251 (mpp) cc_final: 0.6594 (mpp) REVERT: B 213 ARG cc_start: 0.8960 (mtt180) cc_final: 0.7946 (tpp-160) REVERT: B 252 PHE cc_start: 0.9556 (t80) cc_final: 0.8938 (t80) REVERT: B 281 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9366 (mm) REVERT: B 303 PHE cc_start: 0.9354 (t80) cc_final: 0.8455 (t80) REVERT: B 318 TYR cc_start: 0.8188 (t80) cc_final: 0.7817 (t80) REVERT: B 442 MET cc_start: 0.9665 (mmm) cc_final: 0.9445 (tpp) REVERT: B 460 MET cc_start: 0.8448 (mmm) cc_final: 0.7330 (mmm) REVERT: B 506 MET cc_start: 0.8507 (ttm) cc_final: 0.8155 (ttp) REVERT: B 513 MET cc_start: 0.8858 (mmm) cc_final: 0.8642 (mmm) REVERT: B 565 MET cc_start: 0.8865 (ttp) cc_final: 0.8316 (ptt) REVERT: B 580 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9370 (tt) REVERT: B 691 MET cc_start: 0.9103 (mmm) cc_final: 0.8315 (tpp) REVERT: B 726 ASP cc_start: 0.9106 (t70) cc_final: 0.8845 (p0) REVERT: B 913 THR cc_start: 0.9609 (p) cc_final: 0.9384 (t) REVERT: B 950 GLU cc_start: 0.9191 (tt0) cc_final: 0.8972 (mt-10) REVERT: B 998 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.8935 (p0) REVERT: B 1012 PHE cc_start: 0.8248 (t80) cc_final: 0.7641 (t80) REVERT: A 21 MET cc_start: 0.7252 (mpp) cc_final: 0.6597 (mpp) REVERT: A 213 ARG cc_start: 0.8965 (mtt180) cc_final: 0.8109 (mmt-90) REVERT: A 252 PHE cc_start: 0.9555 (t80) cc_final: 0.8933 (t80) REVERT: A 303 PHE cc_start: 0.9356 (t80) cc_final: 0.8453 (t80) REVERT: A 318 TYR cc_start: 0.8182 (t80) cc_final: 0.7812 (t80) REVERT: A 442 MET cc_start: 0.9661 (mmm) cc_final: 0.9437 (tpp) REVERT: A 460 MET cc_start: 0.8432 (mmm) cc_final: 0.7324 (mmm) REVERT: A 513 MET cc_start: 0.8854 (mmm) cc_final: 0.8644 (mmm) REVERT: A 565 MET cc_start: 0.8862 (ttp) cc_final: 0.8315 (ptt) REVERT: A 580 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9363 (tt) REVERT: A 691 MET cc_start: 0.9106 (mmm) cc_final: 0.8316 (tpp) REVERT: A 726 ASP cc_start: 0.9093 (t70) cc_final: 0.8808 (p0) REVERT: A 913 THR cc_start: 0.9615 (p) cc_final: 0.9382 (t) REVERT: A 950 GLU cc_start: 0.9196 (tt0) cc_final: 0.8968 (mt-10) REVERT: A 998 ASP cc_start: 0.9281 (OUTLIER) cc_final: 0.8941 (p0) REVERT: A 1012 PHE cc_start: 0.8088 (t80) cc_final: 0.7852 (t80) REVERT: C 21 MET cc_start: 0.7300 (mpp) cc_final: 0.6650 (mpp) REVERT: C 213 ARG cc_start: 0.8968 (mtt180) cc_final: 0.8056 (tpp-160) REVERT: C 252 PHE cc_start: 0.9496 (t80) cc_final: 0.8912 (t80) REVERT: C 281 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9335 (mm) REVERT: C 303 PHE cc_start: 0.9358 (t80) cc_final: 0.8667 (t80) REVERT: C 442 MET cc_start: 0.9677 (mmm) cc_final: 0.9446 (tpp) REVERT: C 460 MET cc_start: 0.8517 (mmm) cc_final: 0.7496 (mmm) REVERT: C 513 MET cc_start: 0.8902 (mmm) cc_final: 0.8694 (mmm) REVERT: C 565 MET cc_start: 0.8873 (ttp) cc_final: 0.8338 (ptt) REVERT: C 580 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9360 (tt) REVERT: C 691 MET cc_start: 0.9119 (mmm) cc_final: 0.8351 (tpp) REVERT: C 726 ASP cc_start: 0.9092 (t70) cc_final: 0.8840 (p0) REVERT: C 950 GLU cc_start: 0.9177 (tt0) cc_final: 0.8935 (mt-10) REVERT: C 998 ASP cc_start: 0.9273 (OUTLIER) cc_final: 0.8914 (p0) REVERT: C 1012 PHE cc_start: 0.8099 (t80) cc_final: 0.7802 (t80) REVERT: D 21 MET cc_start: 0.7258 (mpp) cc_final: 0.6603 (mpp) REVERT: D 213 ARG cc_start: 0.8972 (mtt180) cc_final: 0.8162 (mmt-90) REVERT: D 252 PHE cc_start: 0.9501 (t80) cc_final: 0.8942 (t80) REVERT: D 303 PHE cc_start: 0.9385 (t80) cc_final: 0.8540 (t80) REVERT: D 318 TYR cc_start: 0.8172 (t80) cc_final: 0.7802 (t80) REVERT: D 460 MET cc_start: 0.8486 (mmm) cc_final: 0.7455 (mmm) REVERT: D 565 MET cc_start: 0.8881 (ttp) cc_final: 0.8449 (ptt) REVERT: D 580 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9375 (tt) REVERT: D 691 MET cc_start: 0.9123 (mmm) cc_final: 0.8352 (tpp) REVERT: D 726 ASP cc_start: 0.9096 (t70) cc_final: 0.8841 (p0) REVERT: D 913 THR cc_start: 0.9598 (p) cc_final: 0.9367 (t) REVERT: D 950 GLU cc_start: 0.9194 (tt0) cc_final: 0.8943 (mt-10) REVERT: D 998 ASP cc_start: 0.9275 (OUTLIER) cc_final: 0.8916 (p0) REVERT: D 1012 PHE cc_start: 0.8106 (t80) cc_final: 0.7789 (t80) outliers start: 55 outliers final: 20 residues processed: 369 average time/residue: 0.1370 time to fit residues: 87.9373 Evaluate side-chains 299 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.060754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046614 restraints weight = 138708.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.048024 restraints weight = 79647.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048919 restraints weight = 54002.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049371 restraints weight = 41012.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.049991 restraints weight = 34993.543| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29172 Z= 0.129 Angle : 0.583 8.758 39580 Z= 0.293 Chirality : 0.042 0.227 4524 Planarity : 0.004 0.048 4984 Dihedral : 5.114 52.480 3848 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.94 % Allowed : 12.44 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3548 helix: -0.21 (0.13), residues: 1476 sheet: -1.57 (0.25), residues: 420 loop : -0.51 (0.17), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 632 TYR 0.010 0.001 TYR C 450 PHE 0.022 0.001 PHE A 832 TRP 0.016 0.001 TRP D 246 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00292 (29172) covalent geometry : angle 0.58326 (39580) hydrogen bonds : bond 0.03378 ( 1072) hydrogen bonds : angle 5.24446 ( 3012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7349 (mpp) cc_final: 0.6695 (mpp) REVERT: B 154 MET cc_start: 0.8002 (mpp) cc_final: 0.7621 (mpp) REVERT: B 213 ARG cc_start: 0.8985 (mtt180) cc_final: 0.7935 (tpp-160) REVERT: B 252 PHE cc_start: 0.9567 (t80) cc_final: 0.8927 (t80) REVERT: B 281 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9303 (mm) REVERT: B 282 MET cc_start: 0.9625 (tpp) cc_final: 0.9146 (tpp) REVERT: B 303 PHE cc_start: 0.9364 (t80) cc_final: 0.8443 (t80) REVERT: B 442 MET cc_start: 0.9681 (mmm) cc_final: 0.9429 (tpp) REVERT: B 565 MET cc_start: 0.8789 (ttp) cc_final: 0.8504 (ttp) REVERT: B 691 MET cc_start: 0.9120 (mmm) cc_final: 0.8495 (tpp) REVERT: B 726 ASP cc_start: 0.9045 (t70) cc_final: 0.8555 (p0) REVERT: B 799 MET cc_start: 0.7794 (tpp) cc_final: 0.7484 (tpp) REVERT: B 830 MET cc_start: 0.8930 (tpp) cc_final: 0.8623 (mmm) REVERT: B 950 GLU cc_start: 0.9181 (tt0) cc_final: 0.8913 (mt-10) REVERT: B 972 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8519 (ppp80) REVERT: B 998 ASP cc_start: 0.9276 (OUTLIER) cc_final: 0.8950 (p0) REVERT: B 1012 PHE cc_start: 0.8259 (t80) cc_final: 0.7945 (t80) REVERT: A 21 MET cc_start: 0.7343 (mpp) cc_final: 0.6691 (mpp) REVERT: A 104 MET cc_start: 0.5283 (mmm) cc_final: 0.4880 (mmm) REVERT: A 154 MET cc_start: 0.8006 (mpp) cc_final: 0.7623 (mpp) REVERT: A 213 ARG cc_start: 0.8993 (mtt180) cc_final: 0.8040 (mmt-90) REVERT: A 252 PHE cc_start: 0.9573 (t80) cc_final: 0.8978 (t80) REVERT: A 282 MET cc_start: 0.9583 (tpp) cc_final: 0.9088 (tpp) REVERT: A 303 PHE cc_start: 0.9363 (t80) cc_final: 0.8690 (t80) REVERT: A 442 MET cc_start: 0.9675 (mmm) cc_final: 0.9418 (tpp) REVERT: A 513 MET cc_start: 0.8780 (mmm) cc_final: 0.8538 (mmt) REVERT: A 565 MET cc_start: 0.8765 (ttp) cc_final: 0.8337 (ttp) REVERT: A 691 MET cc_start: 0.9126 (mmm) cc_final: 0.8499 (tpp) REVERT: A 726 ASP cc_start: 0.9082 (t70) cc_final: 0.8586 (p0) REVERT: A 830 MET cc_start: 0.8915 (mmm) cc_final: 0.8205 (mmm) REVERT: A 913 THR cc_start: 0.9657 (p) cc_final: 0.9408 (t) REVERT: A 950 GLU cc_start: 0.9187 (tt0) cc_final: 0.8914 (mt-10) REVERT: A 972 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8539 (ppp80) REVERT: A 998 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.8943 (p0) REVERT: A 1012 PHE cc_start: 0.8064 (t80) cc_final: 0.7823 (t80) REVERT: C 21 MET cc_start: 0.7371 (mpp) cc_final: 0.6714 (mpp) REVERT: C 154 MET cc_start: 0.7991 (mpp) cc_final: 0.7616 (mpp) REVERT: C 213 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8067 (mmt-90) REVERT: C 252 PHE cc_start: 0.9503 (t80) cc_final: 0.8869 (t80) REVERT: C 281 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9290 (mm) REVERT: C 282 MET cc_start: 0.9627 (tpp) cc_final: 0.9184 (tpp) REVERT: C 303 PHE cc_start: 0.9334 (t80) cc_final: 0.8513 (t80) REVERT: C 442 MET cc_start: 0.9676 (mmm) cc_final: 0.9432 (tpp) REVERT: C 565 MET cc_start: 0.8809 (ttp) cc_final: 0.8401 (ttp) REVERT: C 691 MET cc_start: 0.9123 (mmm) cc_final: 0.8519 (tpp) REVERT: C 726 ASP cc_start: 0.9027 (t70) cc_final: 0.8545 (p0) REVERT: C 830 MET cc_start: 0.8990 (tpp) cc_final: 0.8684 (mmm) REVERT: C 950 GLU cc_start: 0.9176 (tt0) cc_final: 0.8905 (mt-10) REVERT: C 972 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8568 (ppp80) REVERT: C 998 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.8918 (p0) REVERT: C 1012 PHE cc_start: 0.8035 (t80) cc_final: 0.7769 (t80) REVERT: D 21 MET cc_start: 0.7355 (mpp) cc_final: 0.6691 (mpp) REVERT: D 154 MET cc_start: 0.7990 (mpp) cc_final: 0.7612 (mpp) REVERT: D 213 ARG cc_start: 0.9034 (mtt180) cc_final: 0.7987 (tpp-160) REVERT: D 252 PHE cc_start: 0.9515 (t80) cc_final: 0.8954 (t80) REVERT: D 282 MET cc_start: 0.9588 (tpp) cc_final: 0.9086 (tpp) REVERT: D 303 PHE cc_start: 0.9385 (t80) cc_final: 0.8564 (t80) REVERT: D 565 MET cc_start: 0.8816 (ttp) cc_final: 0.8467 (ttp) REVERT: D 691 MET cc_start: 0.9133 (mmm) cc_final: 0.8521 (tpp) REVERT: D 726 ASP cc_start: 0.9047 (t70) cc_final: 0.8567 (p0) REVERT: D 830 MET cc_start: 0.8932 (tpp) cc_final: 0.8644 (mmm) REVERT: D 913 THR cc_start: 0.9655 (p) cc_final: 0.9397 (t) REVERT: D 950 GLU cc_start: 0.9186 (tt0) cc_final: 0.8909 (mt-10) REVERT: D 972 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8539 (ppp80) REVERT: D 998 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8913 (p0) REVERT: D 1012 PHE cc_start: 0.8038 (t80) cc_final: 0.7772 (t80) outliers start: 61 outliers final: 23 residues processed: 318 average time/residue: 0.1481 time to fit residues: 80.0442 Evaluate side-chains 301 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 268 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 311 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.058655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.044658 restraints weight = 141839.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.045979 restraints weight = 81464.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.046976 restraints weight = 54857.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.047573 restraints weight = 41439.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.047844 restraints weight = 33904.914| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 29172 Z= 0.241 Angle : 0.640 7.908 39580 Z= 0.326 Chirality : 0.042 0.161 4524 Planarity : 0.004 0.051 4984 Dihedral : 5.170 52.173 3848 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.03 % Allowed : 12.56 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3548 helix: -0.01 (0.13), residues: 1508 sheet: -1.66 (0.25), residues: 420 loop : -0.36 (0.18), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 742 TYR 0.008 0.001 TYR A 450 PHE 0.027 0.002 PHE B 832 TRP 0.018 0.001 TRP D 246 HIS 0.006 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00511 (29172) covalent geometry : angle 0.63989 (39580) hydrogen bonds : bond 0.03375 ( 1072) hydrogen bonds : angle 5.30791 ( 3012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7433 (mpp) cc_final: 0.6762 (mpp) REVERT: B 104 MET cc_start: 0.5362 (mmm) cc_final: 0.5130 (mmm) REVERT: B 154 MET cc_start: 0.8000 (mpp) cc_final: 0.7610 (mpp) REVERT: B 213 ARG cc_start: 0.9020 (mtt180) cc_final: 0.8036 (mmt-90) REVERT: B 252 PHE cc_start: 0.9631 (t80) cc_final: 0.8863 (t80) REVERT: B 281 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9377 (mm) REVERT: B 282 MET cc_start: 0.9589 (tpp) cc_final: 0.9127 (tpp) REVERT: B 303 PHE cc_start: 0.9319 (t80) cc_final: 0.8607 (t80) REVERT: B 442 MET cc_start: 0.9742 (mmm) cc_final: 0.9496 (tpp) REVERT: B 513 MET cc_start: 0.8673 (mmm) cc_final: 0.8236 (mmt) REVERT: B 580 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9363 (tt) REVERT: B 691 MET cc_start: 0.9171 (mmm) cc_final: 0.8922 (mmm) REVERT: B 799 MET cc_start: 0.7966 (tpp) cc_final: 0.7733 (tpp) REVERT: B 950 GLU cc_start: 0.9183 (tt0) cc_final: 0.8891 (mt-10) REVERT: B 972 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8669 (ppp80) REVERT: B 998 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.8976 (p0) REVERT: A 21 MET cc_start: 0.7427 (mpp) cc_final: 0.6752 (mpp) REVERT: A 154 MET cc_start: 0.8009 (mpp) cc_final: 0.7615 (mpp) REVERT: A 213 ARG cc_start: 0.9017 (mtt180) cc_final: 0.8028 (mmt-90) REVERT: A 252 PHE cc_start: 0.9634 (t80) cc_final: 0.8808 (t80) REVERT: A 282 MET cc_start: 0.9603 (tpp) cc_final: 0.9080 (tpp) REVERT: A 303 PHE cc_start: 0.9318 (t80) cc_final: 0.8524 (t80) REVERT: A 442 MET cc_start: 0.9743 (mmm) cc_final: 0.9495 (tpp) REVERT: A 565 MET cc_start: 0.8812 (ttp) cc_final: 0.8367 (ttp) REVERT: A 580 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9367 (tt) REVERT: A 691 MET cc_start: 0.9170 (mmm) cc_final: 0.8921 (mmm) REVERT: A 830 MET cc_start: 0.9033 (mmm) cc_final: 0.8160 (mmm) REVERT: A 913 THR cc_start: 0.9653 (p) cc_final: 0.9426 (t) REVERT: A 950 GLU cc_start: 0.9203 (tt0) cc_final: 0.8908 (mt-10) REVERT: A 972 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.8682 (ppp80) REVERT: A 998 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8960 (p0) REVERT: C 21 MET cc_start: 0.7463 (mpp) cc_final: 0.6797 (mpp) REVERT: C 104 MET cc_start: 0.5350 (mmm) cc_final: 0.5124 (mmm) REVERT: C 154 MET cc_start: 0.7984 (mpp) cc_final: 0.7600 (mpp) REVERT: C 213 ARG cc_start: 0.9047 (mtt180) cc_final: 0.7921 (tpp-160) REVERT: C 252 PHE cc_start: 0.9605 (t80) cc_final: 0.8964 (t80) REVERT: C 281 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9356 (mm) REVERT: C 282 MET cc_start: 0.9597 (tpp) cc_final: 0.9164 (tpp) REVERT: C 442 MET cc_start: 0.9739 (mmm) cc_final: 0.9490 (tpp) REVERT: C 580 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9360 (tt) REVERT: C 691 MET cc_start: 0.9171 (mmm) cc_final: 0.8922 (mmm) REVERT: C 799 MET cc_start: 0.7474 (tpp) cc_final: 0.7075 (tpp) REVERT: C 950 GLU cc_start: 0.9195 (tt0) cc_final: 0.8900 (mt-10) REVERT: C 972 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8689 (ppp80) REVERT: C 998 ASP cc_start: 0.9264 (OUTLIER) cc_final: 0.8962 (p0) REVERT: D 21 MET cc_start: 0.7448 (mpp) cc_final: 0.6774 (mpp) REVERT: D 104 MET cc_start: 0.5376 (mmm) cc_final: 0.5144 (mmm) REVERT: D 154 MET cc_start: 0.8084 (mpp) cc_final: 0.7718 (mpp) REVERT: D 213 ARG cc_start: 0.9060 (mtt180) cc_final: 0.7919 (tpp-160) REVERT: D 252 PHE cc_start: 0.9595 (t80) cc_final: 0.8741 (t80) REVERT: D 282 MET cc_start: 0.9583 (tpp) cc_final: 0.9220 (tpp) REVERT: D 303 PHE cc_start: 0.9375 (t80) cc_final: 0.8558 (t80) REVERT: D 513 MET cc_start: 0.8729 (mmm) cc_final: 0.8288 (mmt) REVERT: D 580 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9375 (tt) REVERT: D 691 MET cc_start: 0.9181 (mmm) cc_final: 0.8920 (mmm) REVERT: D 913 THR cc_start: 0.9688 (p) cc_final: 0.9449 (t) REVERT: D 950 GLU cc_start: 0.9204 (tt0) cc_final: 0.8901 (mt-10) REVERT: D 972 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8688 (ppp80) REVERT: D 998 ASP cc_start: 0.9270 (OUTLIER) cc_final: 0.8972 (p0) outliers start: 64 outliers final: 29 residues processed: 316 average time/residue: 0.1532 time to fit residues: 81.4724 Evaluate side-chains 292 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 299 optimal weight: 0.2980 chunk 95 optimal weight: 40.0000 chunk 22 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 318 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.058677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.044547 restraints weight = 140880.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.045953 restraints weight = 81903.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.046837 restraints weight = 55196.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.047497 restraints weight = 41906.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.047973 restraints weight = 34034.396| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29172 Z= 0.192 Angle : 0.618 9.412 39580 Z= 0.312 Chirality : 0.042 0.205 4524 Planarity : 0.004 0.049 4984 Dihedral : 5.115 53.029 3848 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.84 % Allowed : 13.64 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3548 helix: 0.11 (0.13), residues: 1508 sheet: -1.70 (0.25), residues: 416 loop : -0.31 (0.18), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 742 TYR 0.009 0.001 TYR A 279 PHE 0.033 0.002 PHE C1012 TRP 0.016 0.001 TRP D 246 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00421 (29172) covalent geometry : angle 0.61768 (39580) hydrogen bonds : bond 0.03298 ( 1072) hydrogen bonds : angle 5.17086 ( 3012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7390 (mpp) cc_final: 0.6686 (mpp) REVERT: B 154 MET cc_start: 0.8104 (mpp) cc_final: 0.7697 (mpp) REVERT: B 213 ARG cc_start: 0.9017 (mtt180) cc_final: 0.8058 (mmt-90) REVERT: B 252 PHE cc_start: 0.9625 (t80) cc_final: 0.8809 (t80) REVERT: B 281 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9406 (mm) REVERT: B 282 MET cc_start: 0.9618 (tpp) cc_final: 0.9163 (tpp) REVERT: B 303 PHE cc_start: 0.9296 (t80) cc_final: 0.8573 (t80) REVERT: B 442 MET cc_start: 0.9701 (mmm) cc_final: 0.9499 (tpp) REVERT: B 513 MET cc_start: 0.8673 (mmm) cc_final: 0.8234 (mmt) REVERT: B 580 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9343 (tt) REVERT: B 726 ASP cc_start: 0.9128 (t70) cc_final: 0.8790 (p0) REVERT: B 799 MET cc_start: 0.8006 (tpp) cc_final: 0.7790 (tpp) REVERT: B 830 MET cc_start: 0.8872 (tpp) cc_final: 0.8310 (mmm) REVERT: B 950 GLU cc_start: 0.9215 (tt0) cc_final: 0.8912 (mt-10) REVERT: B 972 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8707 (ppp80) REVERT: B 998 ASP cc_start: 0.9250 (OUTLIER) cc_final: 0.8947 (p0) REVERT: B 1012 PHE cc_start: 0.8116 (t80) cc_final: 0.7914 (t80) REVERT: A 21 MET cc_start: 0.7376 (mpp) cc_final: 0.6668 (mpp) REVERT: A 154 MET cc_start: 0.8110 (mpp) cc_final: 0.7695 (mpp) REVERT: A 213 ARG cc_start: 0.9015 (mtt180) cc_final: 0.8056 (mmt-90) REVERT: A 252 PHE cc_start: 0.9626 (t80) cc_final: 0.8772 (t80) REVERT: A 282 MET cc_start: 0.9567 (tpp) cc_final: 0.9068 (tpp) REVERT: A 303 PHE cc_start: 0.9296 (t80) cc_final: 0.8526 (t80) REVERT: A 565 MET cc_start: 0.8801 (ttp) cc_final: 0.8212 (ttp) REVERT: A 580 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9370 (tt) REVERT: A 726 ASP cc_start: 0.9152 (t70) cc_final: 0.8797 (p0) REVERT: A 830 MET cc_start: 0.8858 (mmm) cc_final: 0.8354 (mmm) REVERT: A 913 THR cc_start: 0.9706 (p) cc_final: 0.9459 (t) REVERT: A 950 GLU cc_start: 0.9222 (tt0) cc_final: 0.8906 (mt-10) REVERT: A 972 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8715 (ppp80) REVERT: A 998 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8941 (p0) REVERT: C 21 MET cc_start: 0.7409 (mpp) cc_final: 0.6706 (mpp) REVERT: C 154 MET cc_start: 0.8088 (mpp) cc_final: 0.7699 (mpp) REVERT: C 213 ARG cc_start: 0.9049 (mtt180) cc_final: 0.7984 (mmt-90) REVERT: C 252 PHE cc_start: 0.9594 (t80) cc_final: 0.8812 (t80) REVERT: C 281 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9359 (mm) REVERT: C 282 MET cc_start: 0.9636 (tpp) cc_final: 0.9185 (tpp) REVERT: C 303 PHE cc_start: 0.9271 (t80) cc_final: 0.8479 (t80) REVERT: C 580 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9352 (tt) REVERT: C 726 ASP cc_start: 0.9122 (t70) cc_final: 0.8793 (p0) REVERT: C 830 MET cc_start: 0.8880 (tpp) cc_final: 0.8354 (mmm) REVERT: C 950 GLU cc_start: 0.9213 (tt0) cc_final: 0.8922 (mt-10) REVERT: C 972 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.8669 (ppp80) REVERT: C 998 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.8939 (p0) REVERT: D 21 MET cc_start: 0.7397 (mpp) cc_final: 0.6684 (mpp) REVERT: D 154 MET cc_start: 0.8096 (mpp) cc_final: 0.7701 (mpp) REVERT: D 213 ARG cc_start: 0.9050 (mtt180) cc_final: 0.7902 (tpp-160) REVERT: D 252 PHE cc_start: 0.9597 (t80) cc_final: 0.8828 (t80) REVERT: D 282 MET cc_start: 0.9596 (tpp) cc_final: 0.9105 (tpp) REVERT: D 303 PHE cc_start: 0.9344 (t80) cc_final: 0.8596 (t80) REVERT: D 565 MET cc_start: 0.8789 (ttp) cc_final: 0.8563 (tmm) REVERT: D 580 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9362 (tt) REVERT: D 726 ASP cc_start: 0.9128 (t70) cc_final: 0.8796 (p0) REVERT: D 830 MET cc_start: 0.8886 (tpp) cc_final: 0.8352 (mmm) REVERT: D 913 THR cc_start: 0.9700 (p) cc_final: 0.9453 (t) REVERT: D 972 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8665 (ppp80) REVERT: D 998 ASP cc_start: 0.9244 (OUTLIER) cc_final: 0.8939 (p0) outliers start: 58 outliers final: 27 residues processed: 310 average time/residue: 0.1528 time to fit residues: 80.6272 Evaluate side-chains 285 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 11 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 292 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.044940 restraints weight = 139766.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.046305 restraints weight = 80738.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.047222 restraints weight = 54868.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.047740 restraints weight = 41678.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.048358 restraints weight = 33802.521| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29172 Z= 0.134 Angle : 0.599 9.876 39580 Z= 0.299 Chirality : 0.042 0.219 4524 Planarity : 0.004 0.048 4984 Dihedral : 5.027 54.526 3848 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.97 % Allowed : 13.83 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3548 helix: 0.15 (0.13), residues: 1512 sheet: -1.65 (0.26), residues: 416 loop : -0.37 (0.17), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 443 TYR 0.009 0.001 TYR D 279 PHE 0.025 0.001 PHE B1012 TRP 0.013 0.001 TRP D 246 HIS 0.003 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00308 (29172) covalent geometry : angle 0.59927 (39580) hydrogen bonds : bond 0.03253 ( 1072) hydrogen bonds : angle 5.16051 ( 3012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7354 (mpp) cc_final: 0.6626 (mpp) REVERT: B 104 MET cc_start: 0.5333 (mmm) cc_final: 0.5108 (mmm) REVERT: B 154 MET cc_start: 0.8099 (mpp) cc_final: 0.7709 (mpp) REVERT: B 213 ARG cc_start: 0.8986 (mtt180) cc_final: 0.8109 (mmt-90) REVERT: B 252 PHE cc_start: 0.9585 (t80) cc_final: 0.8760 (t80) REVERT: B 281 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9380 (mm) REVERT: B 282 MET cc_start: 0.9608 (tpp) cc_final: 0.9175 (tpp) REVERT: B 303 PHE cc_start: 0.9288 (t80) cc_final: 0.8550 (t80) REVERT: B 580 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9378 (tt) REVERT: B 691 MET cc_start: 0.9170 (mmm) cc_final: 0.8555 (tpp) REVERT: B 726 ASP cc_start: 0.9117 (t70) cc_final: 0.8767 (p0) REVERT: B 799 MET cc_start: 0.7967 (tpp) cc_final: 0.7745 (tpp) REVERT: B 830 MET cc_start: 0.8884 (tpp) cc_final: 0.8291 (mmm) REVERT: B 972 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8643 (ppp80) REVERT: B 998 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8949 (p0) REVERT: A 21 MET cc_start: 0.7349 (mpp) cc_final: 0.6623 (mpp) REVERT: A 104 MET cc_start: 0.5701 (mmm) cc_final: 0.5067 (mmm) REVERT: A 154 MET cc_start: 0.8108 (mpp) cc_final: 0.7711 (mpp) REVERT: A 213 ARG cc_start: 0.8985 (mtt180) cc_final: 0.8109 (mmt-90) REVERT: A 252 PHE cc_start: 0.9625 (t80) cc_final: 0.8903 (t80) REVERT: A 282 MET cc_start: 0.9554 (tpp) cc_final: 0.9061 (tpp) REVERT: A 565 MET cc_start: 0.8831 (ttp) cc_final: 0.8160 (ttp) REVERT: A 580 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9421 (tt) REVERT: A 691 MET cc_start: 0.9193 (mmm) cc_final: 0.8563 (tpp) REVERT: A 726 ASP cc_start: 0.9146 (t70) cc_final: 0.8780 (p0) REVERT: A 830 MET cc_start: 0.8892 (mmm) cc_final: 0.8395 (mmm) REVERT: A 913 THR cc_start: 0.9689 (p) cc_final: 0.9467 (t) REVERT: A 972 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8648 (ppp80) REVERT: A 998 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.8954 (p0) REVERT: C 21 MET cc_start: 0.7377 (mpp) cc_final: 0.6658 (mpp) REVERT: C 104 MET cc_start: 0.5330 (mmm) cc_final: 0.5110 (mmm) REVERT: C 154 MET cc_start: 0.8082 (mpp) cc_final: 0.7701 (mpp) REVERT: C 213 ARG cc_start: 0.9046 (mtt180) cc_final: 0.8025 (mmt-90) REVERT: C 252 PHE cc_start: 0.9593 (t80) cc_final: 0.8801 (t80) REVERT: C 281 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9364 (mm) REVERT: C 282 MET cc_start: 0.9626 (tpp) cc_final: 0.9196 (tpp) REVERT: C 303 PHE cc_start: 0.9271 (t80) cc_final: 0.8468 (t80) REVERT: C 580 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9392 (tt) REVERT: C 691 MET cc_start: 0.9187 (mmm) cc_final: 0.8923 (mmm) REVERT: C 726 ASP cc_start: 0.9118 (t70) cc_final: 0.8773 (p0) REVERT: C 799 MET cc_start: 0.7642 (tpp) cc_final: 0.7417 (tpp) REVERT: C 830 MET cc_start: 0.8889 (tpp) cc_final: 0.8345 (mmm) REVERT: C 972 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8626 (ppp80) REVERT: C 998 ASP cc_start: 0.9262 (OUTLIER) cc_final: 0.8936 (p0) REVERT: D 21 MET cc_start: 0.7369 (mpp) cc_final: 0.6638 (mpp) REVERT: D 104 MET cc_start: 0.5343 (mmm) cc_final: 0.5120 (mmm) REVERT: D 154 MET cc_start: 0.8092 (mpp) cc_final: 0.7702 (mpp) REVERT: D 213 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8002 (mmt-90) REVERT: D 252 PHE cc_start: 0.9594 (t80) cc_final: 0.8956 (t80) REVERT: D 282 MET cc_start: 0.9581 (tpp) cc_final: 0.9074 (tpp) REVERT: D 580 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9393 (tt) REVERT: D 691 MET cc_start: 0.9187 (mmm) cc_final: 0.8914 (mmm) REVERT: D 726 ASP cc_start: 0.9108 (t70) cc_final: 0.8739 (p0) REVERT: D 830 MET cc_start: 0.8848 (tpp) cc_final: 0.8314 (mmm) REVERT: D 913 THR cc_start: 0.9680 (p) cc_final: 0.9444 (t) REVERT: D 972 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.8637 (ppp80) REVERT: D 998 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8938 (p0) outliers start: 62 outliers final: 34 residues processed: 320 average time/residue: 0.1513 time to fit residues: 82.1722 Evaluate side-chains 303 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 340 optimal weight: 0.9990 chunk 320 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN C 157 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.043984 restraints weight = 142540.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.045276 restraints weight = 83142.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.046126 restraints weight = 56829.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.046604 restraints weight = 43464.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.047204 restraints weight = 35607.387| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 29172 Z= 0.222 Angle : 0.665 13.826 39580 Z= 0.332 Chirality : 0.043 0.213 4524 Planarity : 0.004 0.050 4984 Dihedral : 5.071 54.704 3848 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.16 % Allowed : 14.75 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 3548 helix: 0.15 (0.13), residues: 1540 sheet: -1.65 (0.26), residues: 416 loop : -0.42 (0.18), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 113 TYR 0.010 0.001 TYR A 537 PHE 0.020 0.002 PHE D1012 TRP 0.016 0.001 TRP A 246 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00484 (29172) covalent geometry : angle 0.66523 (39580) hydrogen bonds : bond 0.03363 ( 1072) hydrogen bonds : angle 5.33080 ( 3012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 257 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7396 (mpp) cc_final: 0.6662 (mpp) REVERT: B 104 MET cc_start: 0.5674 (mmm) cc_final: 0.5452 (mmm) REVERT: B 154 MET cc_start: 0.8153 (mpp) cc_final: 0.7737 (mpp) REVERT: B 213 ARG cc_start: 0.9043 (mtt180) cc_final: 0.8019 (mmt-90) REVERT: B 252 PHE cc_start: 0.9654 (t80) cc_final: 0.8766 (t80) REVERT: B 282 MET cc_start: 0.9576 (tpp) cc_final: 0.9148 (tpp) REVERT: B 303 PHE cc_start: 0.9304 (t80) cc_final: 0.8557 (t80) REVERT: B 580 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9405 (tt) REVERT: B 830 MET cc_start: 0.8840 (tpp) cc_final: 0.8330 (mmm) REVERT: B 972 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8652 (ppp80) REVERT: B 998 ASP cc_start: 0.9276 (OUTLIER) cc_final: 0.8962 (p0) REVERT: A 21 MET cc_start: 0.7385 (mpp) cc_final: 0.6641 (mpp) REVERT: A 104 MET cc_start: 0.6217 (mmm) cc_final: 0.5686 (mmm) REVERT: A 154 MET cc_start: 0.8167 (mpp) cc_final: 0.7736 (mpp) REVERT: A 213 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8034 (mmt-90) REVERT: A 252 PHE cc_start: 0.9638 (t80) cc_final: 0.8926 (t80) REVERT: A 282 MET cc_start: 0.9532 (tpp) cc_final: 0.9044 (tpp) REVERT: A 565 MET cc_start: 0.8845 (ttp) cc_final: 0.8160 (ttp) REVERT: A 580 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9471 (tt) REVERT: A 913 THR cc_start: 0.9715 (p) cc_final: 0.9488 (t) REVERT: A 972 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.8657 (ppp80) REVERT: A 998 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.8964 (p0) REVERT: C 21 MET cc_start: 0.7406 (mpp) cc_final: 0.6665 (mpp) REVERT: C 104 MET cc_start: 0.5674 (mmm) cc_final: 0.5452 (mmm) REVERT: C 154 MET cc_start: 0.8151 (mpp) cc_final: 0.7736 (mpp) REVERT: C 213 ARG cc_start: 0.9066 (mtt180) cc_final: 0.8036 (mmt-90) REVERT: C 252 PHE cc_start: 0.9603 (t80) cc_final: 0.8950 (t80) REVERT: C 282 MET cc_start: 0.9594 (tpp) cc_final: 0.9171 (tpp) REVERT: C 580 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9374 (tt) REVERT: C 691 MET cc_start: 0.9215 (mmm) cc_final: 0.8940 (mmm) REVERT: C 726 ASP cc_start: 0.9104 (t70) cc_final: 0.8458 (p0) REVERT: C 799 MET cc_start: 0.7737 (tpp) cc_final: 0.7527 (tpp) REVERT: C 830 MET cc_start: 0.8826 (tpp) cc_final: 0.8343 (mmm) REVERT: C 972 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.8669 (ppp80) REVERT: C 998 ASP cc_start: 0.9267 (OUTLIER) cc_final: 0.8947 (p0) REVERT: D 21 MET cc_start: 0.7397 (mpp) cc_final: 0.6649 (mpp) REVERT: D 104 MET cc_start: 0.5685 (mmm) cc_final: 0.5463 (mmm) REVERT: D 154 MET cc_start: 0.8157 (mpp) cc_final: 0.7737 (mpp) REVERT: D 213 ARG cc_start: 0.9072 (mtt180) cc_final: 0.8040 (mmt-90) REVERT: D 252 PHE cc_start: 0.9593 (t80) cc_final: 0.8877 (t80) REVERT: D 282 MET cc_start: 0.9553 (tpp) cc_final: 0.9060 (tpp) REVERT: D 580 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9389 (tt) REVERT: D 691 MET cc_start: 0.9205 (mmm) cc_final: 0.8937 (mmm) REVERT: D 830 MET cc_start: 0.8838 (tpp) cc_final: 0.8365 (mmm) REVERT: D 913 THR cc_start: 0.9704 (p) cc_final: 0.9480 (t) REVERT: D 972 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.8648 (ppp80) REVERT: D 998 ASP cc_start: 0.9266 (OUTLIER) cc_final: 0.8953 (p0) outliers start: 68 outliers final: 45 residues processed: 305 average time/residue: 0.1485 time to fit residues: 77.0119 Evaluate side-chains 297 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 240 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 800 CYS Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 23 optimal weight: 0.3980 chunk 190 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.0270 chunk 200 optimal weight: 5.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN A 451 HIS ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.045683 restraints weight = 137863.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.047004 restraints weight = 80174.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047751 restraints weight = 53758.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.048542 restraints weight = 41389.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.048812 restraints weight = 33493.777| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29172 Z= 0.111 Angle : 0.642 13.301 39580 Z= 0.309 Chirality : 0.043 0.245 4524 Planarity : 0.004 0.046 4984 Dihedral : 4.927 58.032 3848 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 15.58 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.15), residues: 3548 helix: 0.08 (0.13), residues: 1568 sheet: -1.51 (0.26), residues: 408 loop : -0.48 (0.17), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 974 TYR 0.011 0.001 TYR D 279 PHE 0.018 0.001 PHE D1012 TRP 0.012 0.001 TRP B 246 HIS 0.003 0.001 HIS A 693 Details of bonding type rmsd covalent geometry : bond 0.00256 (29172) covalent geometry : angle 0.64208 (39580) hydrogen bonds : bond 0.03264 ( 1072) hydrogen bonds : angle 5.15501 ( 3012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7262 (mpp) cc_final: 0.6504 (mpp) REVERT: B 154 MET cc_start: 0.8070 (mpp) cc_final: 0.7676 (mpp) REVERT: B 213 ARG cc_start: 0.9020 (mtt180) cc_final: 0.8015 (mmt-90) REVERT: B 252 PHE cc_start: 0.9581 (t80) cc_final: 0.8874 (t80) REVERT: B 282 MET cc_start: 0.9566 (tpp) cc_final: 0.9122 (tpp) REVERT: B 513 MET cc_start: 0.8610 (mmm) cc_final: 0.8299 (mmm) REVERT: B 580 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9375 (tt) REVERT: B 691 MET cc_start: 0.9204 (mmm) cc_final: 0.8922 (mmm) REVERT: B 736 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.8524 (t0) REVERT: B 830 MET cc_start: 0.8793 (tpp) cc_final: 0.8271 (mmm) REVERT: B 972 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8609 (ppp80) REVERT: B 998 ASP cc_start: 0.9299 (OUTLIER) cc_final: 0.8942 (p0) REVERT: B 1012 PHE cc_start: 0.8062 (t80) cc_final: 0.7800 (t80) REVERT: A 21 MET cc_start: 0.7262 (mpp) cc_final: 0.6499 (mpp) REVERT: A 104 MET cc_start: 0.6032 (mmm) cc_final: 0.5545 (mmm) REVERT: A 154 MET cc_start: 0.8080 (mpp) cc_final: 0.7679 (mpp) REVERT: A 213 ARG cc_start: 0.8996 (mtt180) cc_final: 0.7964 (mmt-90) REVERT: A 252 PHE cc_start: 0.9573 (t80) cc_final: 0.8855 (t80) REVERT: A 282 MET cc_start: 0.9522 (tpp) cc_final: 0.9036 (tpp) REVERT: A 565 MET cc_start: 0.8912 (ttp) cc_final: 0.8129 (ttp) REVERT: A 580 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9415 (tt) REVERT: A 691 MET cc_start: 0.9223 (mmm) cc_final: 0.8492 (tpp) REVERT: A 913 THR cc_start: 0.9663 (p) cc_final: 0.9449 (t) REVERT: A 972 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8642 (ppp80) REVERT: A 998 ASP cc_start: 0.9304 (OUTLIER) cc_final: 0.8904 (p0) REVERT: A 1012 PHE cc_start: 0.8052 (t80) cc_final: 0.7752 (t80) REVERT: C 21 MET cc_start: 0.7296 (mpp) cc_final: 0.6545 (mpp) REVERT: C 104 MET cc_start: 0.5659 (mmm) cc_final: 0.5436 (mmm) REVERT: C 154 MET cc_start: 0.8060 (mpp) cc_final: 0.7683 (mpp) REVERT: C 213 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8040 (mmt-90) REVERT: C 252 PHE cc_start: 0.9539 (t80) cc_final: 0.8778 (t80) REVERT: C 282 MET cc_start: 0.9589 (tpp) cc_final: 0.9160 (tpp) REVERT: C 303 PHE cc_start: 0.9293 (t80) cc_final: 0.8550 (t80) REVERT: C 513 MET cc_start: 0.8631 (mmm) cc_final: 0.8299 (mmm) REVERT: C 536 MET cc_start: 0.8457 (mtm) cc_final: 0.8209 (mtp) REVERT: C 580 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9372 (tt) REVERT: C 691 MET cc_start: 0.9214 (mmm) cc_final: 0.8493 (tpp) REVERT: C 726 ASP cc_start: 0.9058 (t70) cc_final: 0.8404 (p0) REVERT: C 799 MET cc_start: 0.7713 (tpp) cc_final: 0.7475 (tpp) REVERT: C 819 GLU cc_start: 0.8953 (mp0) cc_final: 0.8697 (mp0) REVERT: C 830 MET cc_start: 0.8795 (tpp) cc_final: 0.8245 (mmm) REVERT: C 913 THR cc_start: 0.9656 (p) cc_final: 0.9441 (t) REVERT: C 972 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8637 (ppp80) REVERT: C 998 ASP cc_start: 0.9293 (OUTLIER) cc_final: 0.8936 (p0) REVERT: D 21 MET cc_start: 0.7283 (mpp) cc_final: 0.6526 (mpp) REVERT: D 154 MET cc_start: 0.8107 (mpp) cc_final: 0.7728 (mpp) REVERT: D 213 ARG cc_start: 0.9039 (mtt180) cc_final: 0.8024 (mmt-90) REVERT: D 252 PHE cc_start: 0.9587 (t80) cc_final: 0.8922 (t80) REVERT: D 282 MET cc_start: 0.9550 (tpp) cc_final: 0.9061 (tpp) REVERT: D 580 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9390 (tt) REVERT: D 691 MET cc_start: 0.9207 (mmm) cc_final: 0.8487 (tpp) REVERT: D 819 GLU cc_start: 0.8978 (mp0) cc_final: 0.8741 (mp0) REVERT: D 830 MET cc_start: 0.8808 (tpp) cc_final: 0.8249 (mmm) REVERT: D 913 THR cc_start: 0.9661 (p) cc_final: 0.9418 (t) REVERT: D 972 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.8634 (ppp80) REVERT: D 998 ASP cc_start: 0.9267 (OUTLIER) cc_final: 0.8915 (p0) REVERT: D 1012 PHE cc_start: 0.8042 (t80) cc_final: 0.7764 (t80) outliers start: 51 outliers final: 33 residues processed: 322 average time/residue: 0.1465 time to fit residues: 80.3461 Evaluate side-chains 297 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 800 CYS Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 153 optimal weight: 0.0980 chunk 177 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 202 optimal weight: 0.0870 chunk 307 optimal weight: 10.0000 chunk 242 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 216 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.060009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.045976 restraints weight = 136636.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.047336 restraints weight = 78976.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.048214 restraints weight = 53179.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048615 restraints weight = 40418.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.049261 restraints weight = 34513.567| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29172 Z= 0.110 Angle : 0.650 10.836 39580 Z= 0.312 Chirality : 0.043 0.225 4524 Planarity : 0.004 0.044 4984 Dihedral : 4.833 58.961 3848 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.46 % Allowed : 16.18 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 3548 helix: 0.05 (0.13), residues: 1592 sheet: -1.43 (0.26), residues: 408 loop : -0.42 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 735 TYR 0.009 0.001 TYR D 279 PHE 0.030 0.001 PHE A 307 TRP 0.011 0.001 TRP D 246 HIS 0.003 0.001 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00250 (29172) covalent geometry : angle 0.65016 (39580) hydrogen bonds : bond 0.03247 ( 1072) hydrogen bonds : angle 5.14161 ( 3012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7423 (mpp) cc_final: 0.6712 (mpp) REVERT: B 104 MET cc_start: 0.6273 (mmm) cc_final: 0.5765 (mmm) REVERT: B 154 MET cc_start: 0.8082 (mpp) cc_final: 0.7682 (mpp) REVERT: B 213 ARG cc_start: 0.9021 (mtt180) cc_final: 0.8004 (mmt-90) REVERT: B 252 PHE cc_start: 0.9568 (t80) cc_final: 0.8860 (t80) REVERT: B 388 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8987 (mm-30) REVERT: B 513 MET cc_start: 0.8610 (mmm) cc_final: 0.8264 (mmm) REVERT: B 565 MET cc_start: 0.8728 (tmm) cc_final: 0.8182 (tmm) REVERT: B 580 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9363 (tt) REVERT: B 691 MET cc_start: 0.9182 (mmm) cc_final: 0.8474 (tpp) REVERT: B 736 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8437 (t0) REVERT: B 972 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8669 (ppp80) REVERT: B 998 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.8937 (p0) REVERT: A 21 MET cc_start: 0.7401 (mpp) cc_final: 0.6685 (mpp) REVERT: A 104 MET cc_start: 0.6179 (mmm) cc_final: 0.5659 (mmm) REVERT: A 154 MET cc_start: 0.8094 (mpp) cc_final: 0.7686 (mpp) REVERT: A 213 ARG cc_start: 0.8866 (mtt180) cc_final: 0.7955 (mmt-90) REVERT: A 252 PHE cc_start: 0.9584 (t80) cc_final: 0.8867 (t80) REVERT: A 282 MET cc_start: 0.9505 (tpp) cc_final: 0.9034 (tpp) REVERT: A 388 GLU cc_start: 0.9368 (mt-10) cc_final: 0.8992 (mm-30) REVERT: A 565 MET cc_start: 0.8857 (ttp) cc_final: 0.8080 (ttp) REVERT: A 580 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9400 (tt) REVERT: A 691 MET cc_start: 0.9171 (mmm) cc_final: 0.8465 (tpp) REVERT: A 913 THR cc_start: 0.9638 (p) cc_final: 0.9393 (t) REVERT: A 972 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8673 (ppp80) REVERT: A 998 ASP cc_start: 0.9335 (OUTLIER) cc_final: 0.8908 (p0) REVERT: C 21 MET cc_start: 0.7429 (mpp) cc_final: 0.6711 (mpp) REVERT: C 154 MET cc_start: 0.8101 (mpp) cc_final: 0.7706 (mpp) REVERT: C 213 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8004 (mmt-90) REVERT: C 252 PHE cc_start: 0.9514 (t80) cc_final: 0.8787 (t80) REVERT: C 282 MET cc_start: 0.9583 (tpp) cc_final: 0.9167 (tpp) REVERT: C 303 PHE cc_start: 0.9299 (t80) cc_final: 0.8560 (t80) REVERT: C 388 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8986 (mm-30) REVERT: C 513 MET cc_start: 0.8546 (mmm) cc_final: 0.8212 (mmm) REVERT: C 536 MET cc_start: 0.8496 (mtm) cc_final: 0.8165 (mtp) REVERT: C 565 MET cc_start: 0.8717 (tmm) cc_final: 0.8208 (tmm) REVERT: C 580 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9366 (tt) REVERT: C 691 MET cc_start: 0.9191 (mmm) cc_final: 0.8470 (tpp) REVERT: C 726 ASP cc_start: 0.9072 (t70) cc_final: 0.8429 (p0) REVERT: C 799 MET cc_start: 0.7926 (tpp) cc_final: 0.7701 (tpp) REVERT: C 830 MET cc_start: 0.8779 (tpp) cc_final: 0.8260 (mmm) REVERT: C 913 THR cc_start: 0.9639 (p) cc_final: 0.9425 (t) REVERT: C 972 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8667 (ppp80) REVERT: C 998 ASP cc_start: 0.9289 (OUTLIER) cc_final: 0.8883 (p0) REVERT: C 1012 PHE cc_start: 0.8142 (t80) cc_final: 0.7936 (t80) REVERT: D 21 MET cc_start: 0.7412 (mpp) cc_final: 0.6689 (mpp) REVERT: D 104 MET cc_start: 0.6324 (mmm) cc_final: 0.5832 (mmm) REVERT: D 154 MET cc_start: 0.8150 (mpp) cc_final: 0.7752 (mpp) REVERT: D 213 ARG cc_start: 0.9034 (mtt180) cc_final: 0.7988 (mmt-90) REVERT: D 252 PHE cc_start: 0.9532 (t80) cc_final: 0.8886 (t80) REVERT: D 282 MET cc_start: 0.9538 (tpp) cc_final: 0.9052 (tpp) REVERT: D 388 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8981 (mm-30) REVERT: D 580 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9392 (tt) REVERT: D 691 MET cc_start: 0.9178 (mmm) cc_final: 0.8461 (tpp) REVERT: D 819 GLU cc_start: 0.8935 (mp0) cc_final: 0.8695 (mp0) REVERT: D 830 MET cc_start: 0.8787 (tpp) cc_final: 0.8263 (mmm) REVERT: D 913 THR cc_start: 0.9639 (p) cc_final: 0.9395 (t) REVERT: D 972 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8635 (ppp80) REVERT: D 998 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.8891 (p0) REVERT: D 1012 PHE cc_start: 0.8161 (t80) cc_final: 0.7895 (t80) outliers start: 46 outliers final: 29 residues processed: 292 average time/residue: 0.1492 time to fit residues: 73.6829 Evaluate side-chains 291 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 185 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 207 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 0.0570 chunk 275 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.057574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.043463 restraints weight = 145273.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.044809 restraints weight = 84483.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.045690 restraints weight = 56022.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.046085 restraints weight = 43273.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.046500 restraints weight = 37040.855| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 29172 Z= 0.254 Angle : 0.735 17.285 39580 Z= 0.359 Chirality : 0.044 0.233 4524 Planarity : 0.004 0.049 4984 Dihedral : 4.965 57.968 3848 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.52 % Allowed : 16.15 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 3548 helix: 0.20 (0.13), residues: 1592 sheet: -1.46 (0.26), residues: 408 loop : -0.31 (0.18), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 735 TYR 0.013 0.002 TYR D 928 PHE 0.026 0.002 PHE B 307 TRP 0.017 0.002 TRP A 246 HIS 0.007 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00549 (29172) covalent geometry : angle 0.73472 (39580) hydrogen bonds : bond 0.03335 ( 1072) hydrogen bonds : angle 5.39887 ( 3012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.77 seconds wall clock time: 62 minutes 28.18 seconds (3748.18 seconds total)